Okay, so sneak attack is normal, coming at levels 1, 5, 9, 13 and 17.
Completely remove the sneak attack that was created for the spellthief class - a different version for each class was needed in 3.5 but not in Pathfinder.
Instead, go to the class tab for the spellthief, and find the "Class Special Abilities" button. Delete all the references there to the sneak attack version you deleted, and add a copy of "Sneak Attack (cSneakAtt)". Now, on that version, press the "Copy" button (one column in from the right), and make 4 copies. Assign one copy to level 5, and one each to 9, 13, and 17.
Now, switch from the editor to the main Hero Lab window and in the develop menu, select "Quick Reload Data Files" (or press ctrl-r). Test your class, and you should have functional sneak attack (if everything else about the class is working).
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